Starting phenix.real_space_refine on Fri Feb 6 13:33:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q1a_72121/02_2026/9q1a_72121_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q1a_72121/02_2026/9q1a_72121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q1a_72121/02_2026/9q1a_72121_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q1a_72121/02_2026/9q1a_72121_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q1a_72121/02_2026/9q1a_72121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q1a_72121/02_2026/9q1a_72121.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Co 2 6.85 5 P 4 5.49 5 S 64 5.16 5 C 7879 2.51 5 N 2082 2.21 5 O 2324 1.98 5 H 12256 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24611 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4030 Classifications: {'peptide': 257} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4013 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 8175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8175 Classifications: {'peptide': 517} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 498} Chain: "D" Number of atoms: 8175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8175 Classifications: {'peptide': 517} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 498} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'B12': 1} Classifications: {'undetermined': 1} Unsupported chir.volume_sign: {'cros': 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'B12': 1} Classifications: {'undetermined': 1} Unsupported chir.volume_sign: {'cros': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'5AD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'5AD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.63, per 1000 atoms: 0.15 Number of scatterers: 24611 At special positions: 0 Unit cell: (158.1, 118.048, 83.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Co 2 26.99 S 64 16.00 P 4 15.00 O 2324 8.00 N 2082 7.00 C 7879 6.00 H 12256 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 729.0 milliseconds 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2846 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 56.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.512A pdb=" N MET A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 134 through 142 removed outlier: 3.645A pdb=" N ILE A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.508A pdb=" N VAL A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'B' and resid 45 through 59 Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 244 through 259 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.561A pdb=" N GLY B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 33 removed outlier: 4.054A pdb=" N PHE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.812A pdb=" N TYR C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 113 through 147 removed outlier: 4.110A pdb=" N ASP C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 177 removed outlier: 4.279A pdb=" N VAL C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 210 through 229 Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 263 through 270 Processing helix chain 'C' and resid 272 through 291 removed outlier: 3.628A pdb=" N PHE C 281 " --> pdb=" O MET C 277 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.983A pdb=" N LEU C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 303' Processing helix chain 'C' and resid 310 through 327 removed outlier: 3.586A pdb=" N VAL C 314 " --> pdb=" O LYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 349 through 365 Processing helix chain 'C' and resid 382 through 400 Processing helix chain 'C' and resid 418 through 436 Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.529A pdb=" N GLU C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 449 through 473 Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 508 through 516 removed outlier: 4.206A pdb=" N ASP C 512 " --> pdb=" O ASN C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 32 removed outlier: 3.903A pdb=" N PHE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.719A pdb=" N TYR D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 113 through 147 removed outlier: 4.238A pdb=" N ASP D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 177 removed outlier: 4.255A pdb=" N VAL D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 210 through 229 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 263 through 269 Processing helix chain 'D' and resid 272 through 291 removed outlier: 3.561A pdb=" N MET D 277 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 281 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 4.040A pdb=" N LEU D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 327 removed outlier: 3.551A pdb=" N VAL D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 349 through 365 Processing helix chain 'D' and resid 382 through 401 Processing helix chain 'D' and resid 418 through 436 Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 449 through 473 Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 508 through 517 removed outlier: 4.009A pdb=" N ASP D 512 " --> pdb=" O ASN D 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 73 removed outlier: 5.724A pdb=" N VAL A 66 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR A 82 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS A 33 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR B 39 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 39 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS B 33 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR B 82 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 66 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 162 removed outlier: 6.740A pdb=" N VAL A 121 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR A 161 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 123 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 122 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU A 185 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 124 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N PHE A 239 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 220 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 162 removed outlier: 3.634A pdb=" N SER B 187 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N PHE B 239 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS B 220 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'C' and resid 335 through 336 removed outlier: 6.081A pdb=" N ILE C 294 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 234 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU C 259 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN C 236 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 181 " --> pdb=" O CYS C 235 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N TYR C 237 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N VAL C 183 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR C 372 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS C 339 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 443 through 445 Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AA8, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.132A pdb=" N ILE D 294 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET D 258 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU D 234 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU D 259 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN D 236 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE D 181 " --> pdb=" O CYS D 235 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N TYR D 237 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N VAL D 183 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR D 372 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N HIS D 339 " --> pdb=" O MET D 373 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 12194 1.08 - 1.33: 2369 1.33 - 1.57: 10136 1.57 - 1.81: 140 1.81 - 2.06: 8 Bond restraints: 24847 Sorted by residual: bond pdb=" C4' LLP B 144 " pdb="H4'1 LLP B 144 " ideal model delta sigma weight residual 0.930 1.112 -0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C4' LLP A 144 " pdb="H4'1 LLP A 144 " ideal model delta sigma weight residual 0.930 1.108 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C6 LLP B 144 " pdb=" H6 LLP B 144 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C6 LLP A 144 " pdb=" H6 LLP A 144 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" N22 B12 A 301 " pdb="CO B12 A 301 " ideal model delta sigma weight residual 1.900 2.058 -0.158 2.00e-02 2.50e+03 6.26e+01 ... (remaining 24842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 44844 4.72 - 9.43: 138 9.43 - 14.15: 20 14.15 - 18.86: 5 18.86 - 23.58: 5 Bond angle restraints: 45012 Sorted by residual: angle pdb=" C4 B12 A 301 " pdb=" N21 B12 A 301 " pdb="CO B12 A 301 " ideal model delta sigma weight residual 109.50 133.08 -23.58 3.00e+00 1.11e-01 6.18e+01 angle pdb=" C16 B12 B 301 " pdb=" N24 B12 B 301 " pdb="CO B12 B 301 " ideal model delta sigma weight residual 109.50 132.82 -23.32 3.00e+00 1.11e-01 6.04e+01 angle pdb=" C4 B12 B 301 " pdb=" N21 B12 B 301 " pdb="CO B12 B 301 " ideal model delta sigma weight residual 109.50 131.18 -21.68 3.00e+00 1.11e-01 5.22e+01 angle pdb=" C16 B12 A 301 " pdb=" N24 B12 A 301 " pdb="CO B12 A 301 " ideal model delta sigma weight residual 109.50 130.27 -20.77 3.00e+00 1.11e-01 4.79e+01 angle pdb=" C6 B12 A 301 " pdb=" N22 B12 A 301 " pdb="CO B12 A 301 " ideal model delta sigma weight residual 109.50 128.62 -19.12 3.00e+00 1.11e-01 4.06e+01 ... (remaining 45007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 11194 35.39 - 70.77: 369 70.77 - 106.16: 24 106.16 - 141.55: 5 141.55 - 176.94: 3 Dihedral angle restraints: 11595 sinusoidal: 6476 harmonic: 5119 Sorted by residual: dihedral pdb=" C3R B12 B 301 " pdb=" O2 B12 B 301 " pdb=" P B12 B 301 " pdb=" O4 B12 B 301 " ideal model delta sinusoidal sigma weight residual 60.00 -145.34 -154.66 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" C3R B12 A 301 " pdb=" O2 B12 A 301 " pdb=" P B12 A 301 " pdb=" O4 B12 A 301 " ideal model delta sinusoidal sigma weight residual 60.00 -145.47 -154.52 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" C38 B12 B 301 " pdb=" C37 B12 B 301 " pdb=" C7 B12 B 301 " pdb=" C8 B12 B 301 " ideal model delta sinusoidal sigma weight residual -59.07 68.13 -127.20 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 11592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.079: 1919 1.079 - 2.158: 0 2.158 - 3.237: 6 3.237 - 4.316: 2 4.316 - 5.395: 2 Chirality restraints: 1929 Sorted by residual: chirality pdb=" C12 B12 B 301 " pdb=" C11 B12 B 301 " pdb=" C46 B12 B 301 " pdb=" C47 B12 B 301 " both_signs ideal model delta sigma weight residual False -2.64 2.75 -5.40 2.00e-01 2.50e+01 7.28e+02 chirality pdb=" C12 B12 A 301 " pdb=" C11 B12 A 301 " pdb=" C46 B12 A 301 " pdb=" C47 B12 A 301 " both_signs ideal model delta sigma weight residual False -2.64 2.75 -5.39 2.00e-01 2.50e+01 7.27e+02 chirality pdb=" N24 B12 A 301 " pdb=" C16 B12 A 301 " pdb=" C19 B12 A 301 " pdb="CO B12 A 301 " both_signs ideal model delta sigma weight residual False -2.93 0.48 -3.41 2.00e-01 2.50e+01 2.91e+02 ... (remaining 1926 not shown) Planarity restraints: 3677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP B 144 " 0.306 2.00e-02 2.50e+03 2.36e-01 6.96e+02 pdb=" NZ LLP B 144 " -0.325 2.00e-02 2.50e+03 pdb=" C4 LLP B 144 " 0.235 2.00e-02 2.50e+03 pdb=" C4' LLP B 144 " -0.127 2.00e-02 2.50e+03 pdb="H4'1 LLP B 144 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 144 " -0.258 2.00e-02 2.50e+03 2.13e-01 5.68e+02 pdb=" NZ LLP A 144 " 0.342 2.00e-02 2.50e+03 pdb=" C4 LLP A 144 " -0.192 2.00e-02 2.50e+03 pdb=" C4' LLP A 144 " 0.072 2.00e-02 2.50e+03 pdb="H4'1 LLP A 144 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 B12 A 301 " -0.128 2.00e-02 2.50e+03 2.13e-01 4.52e+02 pdb=" C18 B12 A 301 " -0.125 2.00e-02 2.50e+03 pdb=" C19 B12 A 301 " 0.368 2.00e-02 2.50e+03 pdb=" N24 B12 A 301 " -0.115 2.00e-02 2.50e+03 ... (remaining 3674 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 8300 2.35 - 2.91: 57905 2.91 - 3.48: 67276 3.48 - 4.04: 92932 4.04 - 4.60: 141195 Nonbonded interactions: 367608 Sorted by model distance: nonbonded pdb=" OP1 LLP B 144 " pdb=" HH TYR D 264 " model vdw 1.789 2.450 nonbonded pdb="HH11 ARG A 154 " pdb=" HG1 THR C 304 " model vdw 1.827 2.100 nonbonded pdb=" H ALA B 132 " pdb=" O44 B12 B 301 " model vdw 1.850 2.450 nonbonded pdb=" H THR A 134 " pdb=" O51 B12 A 301 " model vdw 1.885 2.450 nonbonded pdb=" HG SER C 4 " pdb=" H LEU C 8 " model vdw 1.892 2.100 ... (remaining 367603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 301) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.040 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.158 12593 Z= 0.430 Angle : 1.056 23.578 17072 Z= 0.443 Chirality : 0.257 5.395 1929 Planarity : 0.010 0.226 2188 Dihedral : 16.152 176.937 4770 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.39 % Allowed : 10.77 % Favored : 88.84 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1533 helix: 1.94 (0.19), residues: 786 sheet: -1.23 (0.37), residues: 210 loop : 0.61 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 21 TYR 0.034 0.001 TYR A 146 PHE 0.015 0.001 PHE C 393 TRP 0.002 0.001 TRP C 10 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00765 (12591) covalent geometry : angle 1.05562 (17072) hydrogen bonds : bond 0.13089 ( 649) hydrogen bonds : angle 6.37562 ( 1899) Misc. bond : bond 0.14503 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 256 MET cc_start: 0.8960 (mtm) cc_final: 0.8751 (mtm) REVERT: B 21 ARG cc_start: 0.8919 (ttm-80) cc_final: 0.8558 (ttm110) REVERT: B 73 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: B 102 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8453 (pptt) REVERT: C 243 MET cc_start: 0.9116 (mtm) cc_final: 0.8843 (mtm) REVERT: D 166 ASP cc_start: 0.8905 (m-30) cc_final: 0.8377 (m-30) outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 1.2533 time to fit residues: 115.1540 Evaluate side-chains 82 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 280 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 63 ASN C 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.057432 restraints weight = 88585.535| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.51 r_work: 0.2786 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12593 Z= 0.163 Angle : 0.867 28.295 17072 Z= 0.358 Chirality : 0.088 2.330 1929 Planarity : 0.004 0.055 2188 Dihedral : 11.996 139.120 1836 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.41 % Allowed : 9.29 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.22), residues: 1533 helix: 2.09 (0.18), residues: 787 sheet: -1.06 (0.37), residues: 213 loop : 0.59 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.013 0.001 TYR C 155 PHE 0.013 0.001 PHE C 393 TRP 0.004 0.001 TRP C 10 HIS 0.003 0.001 HIS C 415 Details of bonding type rmsd covalent geometry : bond 0.00360 (12591) covalent geometry : angle 0.86738 (17072) hydrogen bonds : bond 0.04315 ( 649) hydrogen bonds : angle 4.86028 ( 1899) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8634 (mtm110) cc_final: 0.8431 (mtm110) REVERT: B 73 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: B 192 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7771 (pp30) REVERT: C 243 MET cc_start: 0.8917 (mtm) cc_final: 0.8373 (ttp) REVERT: D 166 ASP cc_start: 0.9006 (m-30) cc_final: 0.8473 (m-30) REVERT: D 223 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7971 (mm-30) outliers start: 18 outliers final: 6 residues processed: 93 average time/residue: 1.2329 time to fit residues: 125.7673 Evaluate side-chains 86 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 280 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.831 > 50: distance: 74 - 75: 3.729 distance: 74 - 81: 7.239 distance: 75 - 76: 3.973 distance: 75 - 78: 3.319 distance: 75 - 82: 4.340 distance: 76 - 77: 13.836 distance: 76 - 88: 3.584 distance: 78 - 79: 8.038 distance: 78 - 80: 6.330 distance: 78 - 83: 6.275 distance: 79 - 84: 12.388 distance: 80 - 85: 9.604 distance: 80 - 86: 8.063 distance: 80 - 87: 8.203 distance: 88 - 89: 6.095 distance: 88 - 97: 10.662 distance: 89 - 90: 17.037 distance: 89 - 92: 7.098 distance: 89 - 98: 17.960 distance: 90 - 91: 13.833 distance: 90 - 105: 15.106 distance: 92 - 93: 9.594 distance: 92 - 99: 9.181 distance: 92 - 100: 14.105 distance: 93 - 101: 8.574 distance: 93 - 102: 10.894 distance: 94 - 95: 9.443 distance: 96 - 103: 3.525 distance: 96 - 104: 3.322 distance: 105 - 106: 8.840 distance: 105 - 114: 27.703 distance: 106 - 107: 9.256 distance: 106 - 115: 5.629 distance: 107 - 108: 11.663 distance: 107 - 127: 10.336 distance: 109 - 110: 6.711 distance: 109 - 116: 6.719 distance: 109 - 117: 4.518 distance: 110 - 111: 3.717 distance: 110 - 118: 3.419 distance: 111 - 112: 4.467 distance: 111 - 120: 4.802 distance: 111 - 121: 4.236 distance: 112 - 113: 3.208 distance: 112 - 122: 3.526 distance: 127 - 128: 9.798 distance: 127 - 135: 5.823 distance: 128 - 129: 3.886 distance: 128 - 131: 8.229 distance: 128 - 136: 6.935 distance: 129 - 130: 7.501 distance: 129 - 139: 4.746 distance: 130 - 185: 4.770 distance: 131 - 132: 4.771 distance: 131 - 137: 4.262 distance: 132 - 134: 3.088 distance: 139 - 144: 3.158 distance: 140 - 143: 4.714 distance: 140 - 145: 4.943 distance: 141 - 142: 4.090 distance: 142 - 207: 3.787 distance: 143 - 146: 5.363 distance: 143 - 147: 6.018 distance: 143 - 148: 7.254 distance: 149 - 150: 3.973 distance: 149 - 159: 7.017 distance: 150 - 151: 5.495 distance: 150 - 153: 4.624 distance: 150 - 160: 4.187 distance: 151 - 152: 5.161 distance: 151 - 166: 3.394 distance: 152 - 221: 3.471 distance: 153 - 154: 6.972 distance: 153 - 161: 4.089 distance: 154 - 155: 7.235 distance: 156 - 158: 8.550 distance: 156 - 163: 5.025 distance: 157 - 158: 6.650 distance: 157 - 164: 8.923 distance: 166 - 167: 4.438 distance: 166 - 174: 3.014 distance: 167 - 168: 7.090 distance: 167 - 170: 6.659 distance: 167 - 175: 10.368 distance: 168 - 169: 9.357 distance: 168 - 185: 5.597 distance: 169 - 240: 12.056 distance: 170 - 171: 3.396 distance: 170 - 172: 4.786 distance: 170 - 176: 4.723 distance: 171 - 177: 3.675 distance: 171 - 178: 4.723 distance: 172 - 179: 3.011 distance: 172 - 181: 4.935 distance: 173 - 183: 3.671 distance: 173 - 184: 3.312 distance: 185 - 186: 5.573 distance: 185 - 194: 3.560 distance: 186 - 187: 5.914 distance: 186 - 195: 6.196 distance: 187 - 207: 3.951 distance: 188 - 254: 7.391 distance: 189 - 196: 3.155 distance: 189 - 197: 3.607 distance: 190 - 198: 3.453 distance: 191 - 192: 5.286 distance: 191 - 200: 3.277 distance: 191 - 201: 3.854 distance: 192 - 193: 6.080 distance: 192 - 202: 4.843 distance: 192 - 203: 4.976 distance: 193 - 204: 4.783 distance: 193 - 205: 5.539 distance: 208 - 211: 3.012 distance: 208 - 216: 3.340 distance: 209 - 221: 4.288 distance: 210 - 265: 7.426 distance: 211 - 217: 3.042 distance: 211 - 218: 4.169 distance: 221 - 229: 4.284 distance: 222 - 225: 4.548 distance: 222 - 230: 4.224 distance: 223 - 224: 4.413 distance: 224 - 279: 6.714 distance: 225 - 231: 8.401 distance: 225 - 232: 3.217 distance: 226 - 227: 8.384 distance: 226 - 228: 11.150 distance: 226 - 233: 4.075 distance: 227 - 234: 4.735 distance: 227 - 235: 3.500 distance: 228 - 237: 3.336 distance: 228 - 238: 7.698 distance: 228 - 239: 4.232